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AddOrReplaceReadGroups (Picard)

Assigns all the reads in a file to a single new read-group. This tool accepts INPUT BAM and SAM files or URLs from the Global Alliance for Genomics and Health (GA4GH).

Usage example:

java -jar picard.jar AddOrReplaceReadGroups \ I=input.bam \ O=output.bam \ RGID=4 \ RGLB=lib1 \ RGPL=illumina \ RGPU=unit1 \ RGSM=20

Caveats

The value of the tags must adhere (according to the SAM-spec) with the regex '^[ -~]+$' (one or more characters from the ASCII range 32 through 126). In particular <Space> is the only non-printing character allowed. The program enables only the wholesale assignment of all the reads in the INPUT to a single read-group. If your file already has reads assigned to multiple read-groups, the original RG value will be lost. For more information about read-groups, see the GATK Dictionary entry.

Category Read Data Manipulation


Overview

Assigns all the reads in a file to a single new read-group.

Summary

Many tools (Picard and GATK for example) require or assume the presence of at least one RG tag, defining a "read-group" to which each read can be assigned (as specified in the RG tag in the SAM record). This tool enables the user to assign all the reads in the #INPUT to a single new read-group. For more information about read-groups, see the GATK Dictionary entry.
This tool accepts as INPUT BAM and SAM files or URLs from the Global Alliance for Genomics and Health (GA4GH).

Usage example:

 java -jar picard.jar AddOrReplaceReadGroups \
       I=input.bam \
       O=output.bam \
       RGID=4 \
       RGLB=lib1 \
       RGPL=illumina \
       RGPU=unit1 \
       RGSM=20
 

Caveats

The value of the tags must adhere (according to the SAM-spec) with the regex
#READGROUP_ID_REGEX
(one or more characters from the ASCII range 32 through 126). In particular <Space> is the only non-printing character allowed.
The program enables only the wholesale assignment of all the reads in the #INPUT to a single read-group. If your file already has reads assigned to multiple read-groups, the original RG value will be lost.

AddOrReplaceReadGroups (Picard) specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Required Arguments
--INPUT
 -I
null Input file (BAM or SAM or a GA4GH url).
--OUTPUT
 -O
null Output file (BAM or SAM).
--RGLB
 -LB
null Read-Group library
--RGPL
 -PL
null Read-Group platform (e.g. illumina, solid)
--RGPU
 -PU
null Read-Group platform unit (eg. run barcode)
--RGSM
 -SM
null Read-Group sample name
Optional Tool Arguments
--arguments_file
[] read one or more arguments files and add them to the command line
--help
 -h
false display the help message
--RGCN
 -CN
null Read-Group sequencing center name
--RGDS
 -DS
null Read-Group description
--RGDT
 -DT
null Read-Group run date
--RGFO
 -FO
null Read-Group flow order
--RGID
 -ID
1 Read-Group ID
--RGKS
 -KS
null Read-Group key sequence
--RGPG
 -PG
null Read-Group program group
--RGPI
 -PI
null Read-Group predicted insert size
--RGPM
 -PM
null Read-Group platform model
--SORT_ORDER
 -SO
null Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
--version
false display the version number for this tool
Optional Common Arguments
--COMPRESSION_LEVEL
5 Compression level for all compressed files created (e.g. BAM and VCF).
--CREATE_INDEX
false Whether to create a BAM index when writing a coordinate-sorted BAM file.
--CREATE_MD5_FILE
false Whether to create an MD5 digest for any BAM or FASTQ files created.
--GA4GH_CLIENT_SECRETS
client_secrets.json Google Genomics API client_secrets.json file path.
--MAX_RECORDS_IN_RAM
500000 When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
--QUIET
false Whether to suppress job-summary info on System.err.
--REFERENCE_SEQUENCE
 -R
null Reference sequence file.
--TMP_DIR
[] One or more directories with space available to be used by this program for temporary storage of working files
--USE_JDK_DEFLATER
 -use_jdk_deflater
false Use the JDK Deflater instead of the Intel Deflater for writing compressed output
--USE_JDK_INFLATER
 -use_jdk_inflater
false Use the JDK Inflater instead of the Intel Inflater for reading compressed input
--VALIDATION_STRINGENCY
STRICT Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
--VERBOSITY
INFO Control verbosity of logging.
Advanced Arguments
--showHidden
false display hidden arguments

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.


--arguments_file / NA

read one or more arguments files and add them to the command line

List[File]  []


--COMPRESSION_LEVEL / NA

Compression level for all compressed files created (e.g. BAM and VCF).

int  5  [ [ -∞  ∞ ] ]


--CREATE_INDEX / NA

Whether to create a BAM index when writing a coordinate-sorted BAM file.

Boolean  false


--CREATE_MD5_FILE / NA

Whether to create an MD5 digest for any BAM or FASTQ files created.

boolean  false


--GA4GH_CLIENT_SECRETS / NA

Google Genomics API client_secrets.json file path.

String  client_secrets.json


--help / -h

display the help message

boolean  false


--INPUT / -I

Input file (BAM or SAM or a GA4GH url).

R String  null


--MAX_RECORDS_IN_RAM / NA

When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.

Integer  500000  [ [ -∞  ∞ ] ]


--OUTPUT / -O

Output file (BAM or SAM).

R File  null


--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean  false


--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null


--RGCN / -CN

Read-Group sequencing center name

String  null


--RGDS / -DS

Read-Group description

String  null


--RGDT / -DT

Read-Group run date

Iso8601Date  null


--RGFO / -FO

Read-Group flow order

String  null


--RGID / -ID

Read-Group ID

String  1


--RGKS / -KS

Read-Group key sequence

String  null


--RGLB / -LB

Read-Group library

R String  null


--RGPG / -PG

Read-Group program group

String  null


--RGPI / -PI

Read-Group predicted insert size

Integer  null


--RGPL / -PL

Read-Group platform (e.g. illumina, solid)

R String  null


--RGPM / -PM

Read-Group platform model

String  null


--RGPU / -PU

Read-Group platform unit (eg. run barcode)

R String  null


--RGSM / -SM

Read-Group sample name

R String  null


--showHidden / -showHidden

display hidden arguments

boolean  false


--SORT_ORDER / -SO

Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.

The --SORT_ORDER argument is an enumerated type (SortOrder), which can have one of the following values:

unsorted
queryname
coordinate
duplicate
unknown

SortOrder  null


--TMP_DIR / NA

One or more directories with space available to be used by this program for temporary storage of working files

List[File]  []


--USE_JDK_DEFLATER / -use_jdk_deflater

Use the JDK Deflater instead of the Intel Deflater for writing compressed output

Boolean  false


--USE_JDK_INFLATER / -use_jdk_inflater

Use the JDK Inflater instead of the Intel Inflater for reading compressed input

Boolean  false


--VALIDATION_STRINGENCY / NA

Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.

The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:

STRICT
LENIENT
SILENT

ValidationStringency  STRICT


--VERBOSITY / NA

Control verbosity of logging.

The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:

ERROR
WARNING
INFO
DEBUG

LogLevel  INFO


--version / NA

display the version number for this tool

boolean  false


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GATK version 4.0.3.0 built at 09-43-2018 09:43:10.